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GitHub topics: gotoh

lignum-vitae/goombay

Python implementation of several sequence alignment algorithms such as Waterman-Smith-Beyer, Gotoh, and Needleman-Wunsch intended to calculate distance, show alignment, and display the underlying matrices.

Language: Python - Size: 217 KB - Last synced at: 19 days ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

github4touchdouble/bench-sequence-alignments

Benchmark the performance of sequence alignment workflows

Language: Ruby - Size: 16.6 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

RJPenic/OSALG

Optimal Sequence Aligner allowing for Long Gaps

Language: C++ - Size: 80.1 KB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0

odoluca/Fast-NW-and-SW-Pairwise-alignment-using-numba-JIT

This project includes Needleman-Wunsch and Smith-Waterman algorithms and their afine gap variations (Gotoh) written to work with Cython, PyPy and Numba. Numba JIT shows greater performance. For Best performance use gotoh_jit.py to get only the best score and use gotoh_jit_traceback to get the best alignment

Language: Python - Size: 232 KB - Last synced at: 2 months ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 2

Related Keywords
gotoh 4 smith-waterman 3 sequence-alignment 3 needleman-wunsch 3 gotoh-algorithm 2 alignment 2 python-3-6 1 python 1 pypy3 1 protein-sequences 1 pairwise-alignment 1 pairwise 1 numba 1 dna-sequences 1 cython 1 simd 1 bioinformatics 1 protein-alignment 1 shortest-common-supersequence 1 hamming-distance 1 longest-common-subsequence 1 levenshtein-distance 1 jaro-winkler 1 jaro 1 hirschberg 1